Novartis Diagnostics, the unit of the giant healthcare company that tests the safety of 80 percent of the U.S. blood supply, has struck a deal to get access to Quanterix’s technology in Cambridge. Novartis plans to run tests to see how good the Quanterix instrument is at finding a rare protein biomarker in the blood associated with an undisclosed neurological disorder. Terms of the partnership aren’t being disclosed.

“We’re starting with one target, but we’re talking about looking at a few others,” says Quanterix CEO Dave Okrongly. “I hope this will grow into a close relationship that builds over time. Novartis has a lot of interest in accessing new technology, and when they looked at what Quanterix has to offer, they saw it gives them an edge they can’t get with other protein measurement technologies.”

Quanterix, started in 2007 by Tufts University chemist David Walt (the founder of San Diego-based Illumina (NASDAQ: ILMN), has been on our radar since its early days. The big idea is to create an instrument that measures proteins in a way that’s 1,000 times more sensitive than standard Elisa tests, made by big players like Abbott Laboratories (NYSE: ABT) and Becton Dickinson (NYSE: BDX). Those standard tests are made to detect antibodies in a blood sample that show whether a patient has been exposed to HIV, hepatitis C, or other pathogens. Quanterix was off and running in August 2008 when it snagged a $15 million financing from Arch Venture Partners, Bain Capital Ventures, and Flagship Ventures.

While building the tool, hammering out technical issues to ensure it generates precise and reproducible results, the company has also sought to prove its value for biomedical research. The company generated a lot of attention last June when it published research in Nature Biotechnology that showed it was more effective than Elisa at spotting prostate specific antigen (PSA), the common diagnostic marker for prostate cancer. That paper triggered a number of inquiries from academic researchers, and a few from industrial scientists, who wanted to get access to the Quanterix technology to see if it could find novel biomarkers which are thought to be correlated with disease, Okrongly says.

Dave Okrongly

Quanterix isn’t ready to commercialize this instrument—that day won’t come until late 2012 or early 2013, Okrongly says. So for now, the company is keeping its fledgling technology inside its walls, while providing select academic and industrial scientists access in a number of different settings. So getting an organization like Novartis could be quite valuable if the first test pans out, because like Okrongly says, it could lead to more uses.

“The most important thing it represents is a shot on goal,” Okrongly says.

Getting a shot is really all a startup can ask for in what’s a pretty darn tough financing environment. Since the original $15 million financing, Quanterix has pulled in a $2.5 million bridge loan, and one other partnership with an undisclosed big company, Okrongly says. Last month, when I met him at the JP Morgan Healthcare Conference in San Francisco, he said he hoped to do a few of these partnerships to help validate the technology, bring in some cash, and pave the way for a Series B venture financing later in 2011.

So I figure it’s fair to say a lot is riding on this year’s battery of trial runs. “Such a big opportunity is waiting for us,” Okrongly says. “We have a lot of people coming to us who want access.”